Calcium in PDB 6epy: Structure of the Pbp Melb (ATU4661) in Complex with Raffinose From A.Fabrum C58

The structure of Structure of the Pbp Melb (ATU4661) in Complex with Raffinose From A.Fabrum C58, PDB code: 6epy was solved by S.Morera, A.Vigouroux, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.14 / 2.04
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	354.300, 74.270, 108.220, 90.00, 105.50, 90.00
R / Rfree (%)	17.4 / 20

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 50; Page 6, Binding sites: 51 - 60; Page 7, Binding sites: 61 - 70; Page 8, Binding sites: 71 - 80; Page 9, Binding sites: 81 - 90; Page 10, Binding sites: 91 - 100; Page 11, Binding sites: 101 - 110; Page 12, Binding sites: 111 - 120; Page 13, Binding sites: 121 - 125;

Binding sites:

The binding sites of Calcium atom in the Structure of the Pbp Melb (ATU4661) in Complex with Raffinose From A.Fabrum C58 (pdb code 6epy). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 125 binding sites of Calcium where determined in the Structure of the Pbp Melb (ATU4661) in Complex with Raffinose From A.Fabrum C58, PDB code: 6epy:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 125 in the Structure of the Pbp Melb (ATU4661) in Complex with Raffinose From A.Fabrum C58


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of the Pbp Melb (ATU4661) in Complex with Raffinose From A.Fabrum C58 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca704 b:41.8 occ:1.00 O A:HOH1131 2.3 43.0 1.0 O A:HOH833 2.4 38.8 1.0 O A:HOH848 2.4 35.4 1.0 O A:HOH831 2.4 31.1 1.0 O A:HOH826 2.5 38.9 1.0 O A:HOH919 2.7 35.4 1.0 O A:ALA169 4.1 31.7 1.0 OG A:SER240 4.3 33.9 1.0 CB A:HIS241 4.4 32.4 1.0 OD1 A:ASN171 4.5 29.3 1.0 CB A:ASP173 4.7 35.5 1.0 OD2 A:ASP174 4.7 31.4 1.0 OD1 A:ASP174 4.7 31.0 1.0 OD2 A:ASP173 4.7 51.9 1.0 ND1 A:HIS241 4.8 36.4 1.0 ND2 A:ASN171 4.8 35.1 1.0 N A:HIS241 4.9 29.7 1.0 CG A:HIS241 4.9 35.0 1.0

Calcium binding site 2 out of 125 in the Structure of the Pbp Melb (ATU4661) in Complex with Raffinose From A.Fabrum C58


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of the Pbp Melb (ATU4661) in Complex with Raffinose From A.Fabrum C58 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca705 b:33.8 occ:1.00 O A:ASP185 2.3 35.2 1.0 O A:VAL188 2.3 34.7 1.0 O A:VAL183 2.3 33.2 1.0 O A:HOH922 2.4 33.2 1.0 O A:ALA182 2.4 32.7 1.0 O A:HOH956 2.4 39.1 1.0 O A:HOH1017 2.7 39.0 1.0 C A:VAL183 3.3 34.9 1.0 C A:ASP185 3.4 38.5 1.0 C A:VAL188 3.6 34.1 1.0 C A:ALA182 3.6 34.2 1.0 CA A:VAL183 3.8 29.8 1.0 N A:VAL183 4.1 29.6 1.0 N A:ASP185 4.2 34.9 1.0 CA A:PRO186 4.2 36.7 1.0 N A:PRO186 4.3 37.8 1.0 C A:VAL184 4.3 38.1 1.0 N A:VAL188 4.3 33.4 1.0 CA A:ASP185 4.3 34.9 1.0 N A:VAL184 4.3 33.6 1.0 CA A:VAL188 4.4 32.5 1.0 O A:HOH1095 4.4 35.5 1.0 O A:VAL184 4.4 36.6 1.0 N A:SER189 4.5 30.7 1.0 C A:PRO186 4.6 40.9 1.0 CA A:SER189 4.6 30.7 1.0 CB A:VAL188 4.7 35.7 1.0 O A:HOH1154 4.7 46.7 1.0 CA A:ALA182 4.8 30.9 1.0 OG A:SER189 4.8 47.6 1.0 O A:ALA195 4.8 31.4 1.0 CA A:VAL184 4.8 35.1 1.0 CB A:ASP185 4.8 36.3 1.0 CD A:PRO190 4.9 32.8 1.0 N A:ASN187 4.9 36.3 1.0

Calcium binding site 3 out of 125 in the Structure of the Pbp Melb (ATU4661) in Complex with Raffinose From A.Fabrum C58


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of the Pbp Melb (ATU4661) in Complex with Raffinose From A.Fabrum C58 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca706 b:52.4 occ:1.00 OD1 A:ASP410 2.3 53.0 1.0 O A:HOH1134 2.3 45.5 1.0 O A:HOH912 2.5 51.9 1.0 O A:HOH926 2.5 34.8 1.0 O A:HOH925 2.5 37.0 1.0 O A:HOH900 2.6 48.9 1.0 CG A:ASP410 3.5 54.3 1.0 OD2 A:ASP410 4.3 61.8 1.0 OG1 A:THR418 4.3 40.0 1.0 N A:ASP410 4.4 39.4 1.0 O A:HOH917 4.4 39.6 1.0 O A:HOH1140 4.4 53.1 1.0 CA A:ASP410 4.5 40.1 1.0 CB A:ASP410 4.6 42.7 1.0 O A:GLY415 4.6 44.0 1.0 O A:LYS406 4.6 38.3 1.0 CA A:CA709 4.8 47.1 1.0 C A:GLY409 4.8 40.8 1.0 O A:HOH1130 4.9 47.1 1.0 O A:VAL413 4.9 41.8 1.0 CA A:CA727 4.9 76.4 1.0 O A:HOH960 5.0 41.4 1.0

Calcium binding site 4 out of 125 in the Structure of the Pbp Melb (ATU4661) in Complex with Raffinose From A.Fabrum C58


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of the Pbp Melb (ATU4661) in Complex with Raffinose From A.Fabrum C58 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca707 b:38.1 occ:1.00 O A:PHE464 2.2 42.0 1.0 OD1 A:ASP462 2.3 49.5 1.0 OD1 A:ASP460 2.3 50.9 1.0 OD1 A:ASN476 2.3 37.9 1.0 OD1 A:ASP458 2.4 51.8 1.0 ND2 A:ASN466 2.4 38.0 1.0 CG A:ASP460 3.2 55.1 1.0 CG A:ASP462 3.3 48.6 1.0 C A:PHE464 3.3 41.7 1.0 CG A:ASN476 3.4 46.8 1.0 CG A:ASN466 3.5 50.9 1.0 CG A:ASP458 3.5 51.7 1.0 OD2 A:ASP460 3.5 59.9 1.0 ND2 A:ASN476 3.7 46.6 1.0 OD2 A:ASP462 3.8 47.0 1.0 OD1 A:ASN466 3.9 42.5 1.0 N A:PHE464 3.9 42.0 1.0 CA A:PHE464 3.9 39.4 1.0 CB A:PHE464 4.1 40.4 1.0 CA A:ASP458 4.2 45.9 1.0 CB A:ASP458 4.2 47.1 1.0 N A:ASP460 4.3 50.2 1.0 N A:ASP462 4.3 49.3 1.0 N A:LEU465 4.4 37.6 1.0 N A:THR459 4.4 48.5 1.0 OD2 A:ASP458 4.4 54.6 1.0 CB A:ASP462 4.5 47.6 1.0 CB A:ASP460 4.5 50.6 1.0 C A:LEU465 4.5 41.2 1.0 N A:ASN466 4.5 39.5 1.0 C A:ASP458 4.7 51.7 1.0 CA A:LEU465 4.7 37.8 1.0 CB A:ASN466 4.7 37.0 1.0 CB A:ASN476 4.7 35.0 1.0 O A:LEU465 4.7 38.5 1.0 CA A:ASP460 4.7 50.4 1.0 CA A:ASP462 4.7 47.2 1.0 N A:GLY463 4.8 46.7 1.0 N A:GLY461 4.9 54.0 1.0 C A:ASP462 4.9 49.1 1.0 C A:ASP460 4.9 55.5 1.0

Calcium binding site 5 out of 125 in the Structure of the Pbp Melb (ATU4661) in Complex with Raffinose From A.Fabrum C58


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structure of the Pbp Melb (ATU4661) in Complex with Raffinose From A.Fabrum C58 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca708 b:58.8 occ:1.00 NE1 A:TRP179 3.1 37.3 1.0 N A:LEU206 3.5 39.4 1.0 CA A:THR205 3.5 37.9 1.0 CB A:THR205 3.7 45.9 1.0 O A:LEU206 3.9 43.9 1.0 CD1 A:TRP179 4.0 37.6 1.0 NZ D:LYS457 4.1 1.0 1.0 CE D:LYS469 4.1 0.8 1.0 CE2 A:TRP179 4.1 37.8 1.0 C A:THR205 4.1 41.6 1.0 NZ D:LYS469 4.1 0.9 1.0 CG2 A:THR205 4.2 46.2 1.0 CE D:LYS457 4.2 0.4 1.0 O A:THR204 4.3 41.4 1.0 CZ2 A:TRP179 4.4 37.5 1.0 CA A:LEU206 4.6 38.0 1.0 C A:LEU206 4.6 43.7 1.0 CG2 A:VAL184 4.7 38.5 1.0 N A:THR205 4.7 37.5 1.0 OG1 A:THR205 4.9 48.6 1.0 C A:THR204 5.0 41.9 1.0

Calcium binding site 6 out of 125 in the Structure of the Pbp Melb (ATU4661) in Complex with Raffinose From A.Fabrum C58


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Structure of the Pbp Melb (ATU4661) in Complex with Raffinose From A.Fabrum C58 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca709 b:47.1 occ:1.00 O A:HOH925 3.0 37.0 1.0 O A:HOH950 3.0 39.3 1.0 OG1 A:THR418 3.1 40.0 1.0 O A:HOH1162 3.4 43.7 1.0 O A:HOH1134 3.4 45.5 1.0 C A:THR418 3.7 37.2 1.0 C A:ALA419 3.7 33.3 1.0 N A:ALA419 3.8 31.9 1.0 O A:THR418 3.8 36.5 1.0 CB A:THR418 3.8 37.6 1.0 CD1 A:ILE420 3.9 38.5 1.0 CA A:ALA419 3.9 30.9 1.0 N A:ILE420 3.9 30.4 1.0 O A:ALA419 4.1 31.8 1.0 CA A:GLY409 4.4 36.9 1.0 CA A:THR418 4.4 32.8 1.0 CG1 A:ILE420 4.4 33.9 1.0 O A:ARG405 4.4 33.1 1.0 CA A:ILE420 4.6 29.2 1.0 CA A:LYS406 4.6 33.8 1.0 O A:HOH917 4.7 39.6 1.0 CA A:CA706 4.8 52.4 1.0 O A:HOH926 4.8 34.8 1.0 O A:LYS406 4.8 38.3 1.0 CA A:CA734 4.9 68.7 1.0 N A:GLY409 5.0 35.8 1.0

Calcium binding site 7 out of 125 in the Structure of the Pbp Melb (ATU4661) in Complex with Raffinose From A.Fabrum C58


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Structure of the Pbp Melb (ATU4661) in Complex with Raffinose From A.Fabrum C58 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca710 b:72.1 occ:1.00 O A:PRO248 2.2 48.3 1.0 O A:HOH899 2.3 46.7 1.0 O A:SER251 2.5 46.8 1.0 C A:PRO248 3.4 47.4 1.0 C A:SER251 3.7 48.2 1.0 CA A:PRO248 4.1 41.3 1.0 N A:LYS249 4.5 44.3 1.0 CA A:LYS252 4.5 48.7 1.0 N A:SER251 4.5 45.5 1.0 CB A:PRO248 4.5 42.4 1.0 N A:LYS252 4.5 47.0 1.0 O A:ASN253 4.7 45.6 1.0 CA A:LYS249 4.7 45.6 1.0 CA A:SER251 4.8 44.5 1.0 C A:LYS249 4.8 50.4 1.0 C A:LYS252 4.9 53.8 1.0

Calcium binding site 8 out of 125 in the Structure of the Pbp Melb (ATU4661) in Complex with Raffinose From A.Fabrum C58


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Structure of the Pbp Melb (ATU4661) in Complex with Raffinose From A.Fabrum C58 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca711 b:41.8 occ:1.00 O A:HOH913 2.9 31.5 1.0 O A:HOH1047 3.1 29.8 1.0 N A:GLY76 3.3 29.5 1.0 O A:HOH1001 3.5 51.0 1.0 CA A:GLY76 3.6 29.8 1.0 CB A:LYS74 4.0 31.9 1.0 OE1 A:GLU299 4.1 38.3 1.0 N A:THR75 4.3 30.8 1.0 CE A:LYS74 4.4 36.8 1.0 NZ A:LYS74 4.4 53.4 1.0 C A:THR75 4.5 34.0 1.0 C A:LYS74 4.5 33.8 1.0 O A:HOH935 4.7 29.4 1.0 CA A:LYS74 4.7 30.0 1.0 C A:GLY76 4.8 33.5 1.0 CG A:LYS74 4.8 34.2 1.0 CA A:THR75 4.9 30.8 1.0 CD A:GLU299 5.0 51.9 1.0

Calcium binding site 9 out of 125 in the Structure of the Pbp Melb (ATU4661) in Complex with Raffinose From A.Fabrum C58


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Structure of the Pbp Melb (ATU4661) in Complex with Raffinose From A.Fabrum C58 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca712 b:41.1 occ:1.00 O A:HOH1115 3.2 36.0 1.0 NE1 A:TRP48 3.2 30.7 1.0 OD1 A:ASN308 3.2 39.4 1.0 CD1 A:TRP48 3.6 32.1 1.0 CB A:TYR85 3.9 28.5 1.0 CB A:PRO46 4.0 30.7 1.0 ND2 A:ASN308 4.1 25.4 1.0 CG A:ASN308 4.1 36.2 1.0 N A:GLY86 4.3 28.0 1.0 CA A:GLY86 4.4 27.2 1.0 C A:TYR85 4.4 30.6 1.0 CE2 A:TRP48 4.5 31.4 1.0 CG A:PRO46 4.5 33.6 1.0 O A:HOH804 4.6 29.1 1.0 O A:TYR85 4.7 28.7 1.0 O A:HOH810 4.7 39.7 1.0 CA A:CA714 4.8 63.5 1.0 CA A:TYR85 4.8 27.9 1.0 O A:HOH1072 4.9 52.0 1.0 CG A:TYR85 4.9 26.9 1.0 CA A:PRO46 4.9 29.3 1.0 CG A:TRP48 5.0 29.9 1.0

Calcium binding site 10 out of 125 in the Structure of the Pbp Melb (ATU4661) in Complex with Raffinose From A.Fabrum C58


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Structure of the Pbp Melb (ATU4661) in Complex with Raffinose From A.Fabrum C58 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca713 b:71.0 occ:1.00 O A:GLU672 2.8 64.6 1.0 N A:MSE267 3.1 39.6 1.0 C A:GLY671 3.2 53.0 1.0 O A:GLY671 3.3 54.2 1.0 CE A:MSE267 3.5 71.6 1.0 O A:HOH1086 3.5 54.3 1.0 N A:GLU672 3.5 53.2 1.0 CA A:GLY671 3.6 43.3 1.0 CB A:MSE267 3.6 46.5 1.0 C A:GLU672 3.8 65.5 1.0 CA A:MSE267 3.9 41.4 1.0 O A:GLU265 3.9 40.5 1.0 CA A:TYR266 4.0 37.7 1.0 C A:TYR266 4.0 41.2 1.0 CA A:GLU672 4.1 56.6 1.0 CG A:MSE267 4.2 58.4 1.0 N A:GLY671 4.3 40.4 1.0 O A:MSE267 4.4 38.2 1.0 SE A:MSE267 4.6 73.9 1.0 C A:MSE267 4.6 39.6 1.0 C A:GLU265 4.8 41.3 1.0 N A:TYR266 4.8 38.0 1.0 CG A:TYR266 4.9 38.2 1.0

T.Meyer, A.Vigouroux, M.Aumont-Nicaise, G.Comte, L.Vial, C.Lavire, S.Morera. The Plant Defense Signal Galactinol Is Specifically Used As A Nutrient By the Bacterial Pathogenagrobacterium Fabrum. J. Biol. Chem. V. 293 7930 2018.
ISSN: ESSN 1083-351X
PubMed: 29602905
DOI: 10.1074/JBC.RA118.001856